Multiple sequence alignment - TraesCS7B01G454300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G454300 chr7B 100.000 3574 0 0 1 3574 715084314 715080741 0.000000e+00 6601
1 TraesCS7B01G454300 chr7B 98.577 3584 39 7 1 3574 715156390 715152809 0.000000e+00 6325
2 TraesCS7B01G454300 chr7B 98.465 3584 44 6 1 3574 715123710 715120128 0.000000e+00 6303
3 TraesCS7B01G454300 chr7B 96.765 3586 67 13 2 3574 714902014 714898465 0.000000e+00 5934
4 TraesCS7B01G454300 chr7B 97.797 1770 25 4 1813 3574 714947476 714945713 0.000000e+00 3040
5 TraesCS7B01G454300 chr7B 86.901 1794 156 34 812 2575 715322453 715320709 0.000000e+00 1938
6 TraesCS7B01G454300 chr7B 95.678 1180 38 7 644 1815 714950521 714949347 0.000000e+00 1884
7 TraesCS7B01G454300 chr7B 93.153 628 26 5 2348 2973 714845000 714844388 0.000000e+00 905
8 TraesCS7B01G454300 chr7B 96.936 359 11 0 3037 3395 714844385 714844027 1.420000e-168 603
9 TraesCS7B01G454300 chr7B 90.608 181 14 3 1 179 714950696 714950517 1.660000e-58 237
10 TraesCS7B01G454300 chr7B 89.326 178 1 2 3397 3574 714843991 714843832 1.300000e-49 207
11 TraesCS7B01G454300 chr4A 93.913 2218 86 20 644 2850 700430228 700428049 0.000000e+00 3302
12 TraesCS7B01G454300 chr4A 96.610 118 4 0 62 179 700430341 700430224 2.810000e-46 196
13 TraesCS7B01G454300 chr4A 98.529 68 1 0 1 68 700430978 700430911 1.740000e-23 121
14 TraesCS7B01G454300 chr7D 87.039 1844 164 47 769 2572 619581941 619583749 0.000000e+00 2012
15 TraesCS7B01G454300 chr7D 86.272 1843 169 48 769 2572 620583009 620584806 0.000000e+00 1925
16 TraesCS7B01G454300 chr7D 93.852 553 18 8 2850 3395 495333978 495333435 0.000000e+00 819
17 TraesCS7B01G454300 chr7D 93.231 458 23 5 1084 1541 619359201 619358752 0.000000e+00 667
18 TraesCS7B01G454300 chr7D 91.455 433 24 9 730 1160 619359590 619359169 1.850000e-162 582
19 TraesCS7B01G454300 chr7D 95.028 181 5 2 3398 3574 495333398 495333218 7.550000e-72 281
20 TraesCS7B01G454300 chr7D 87.500 160 19 1 21 179 619384479 619384320 2.190000e-42 183
21 TraesCS7B01G454300 chr7A 86.818 1851 172 37 769 2572 713833345 713835170 0.000000e+00 2001
22 TraesCS7B01G454300 chrUn 87.303 1394 113 39 734 2096 93249919 93248559 0.000000e+00 1535
23 TraesCS7B01G454300 chr1D 92.208 462 34 2 181 641 483885861 483886321 0.000000e+00 652
24 TraesCS7B01G454300 chr1D 91.416 466 38 2 178 642 35755962 35756426 3.890000e-179 638
25 TraesCS7B01G454300 chr4D 92.191 461 34 2 184 643 4343376 4342917 0.000000e+00 651
26 TraesCS7B01G454300 chr4D 91.991 462 32 4 181 641 494790352 494789895 0.000000e+00 643
27 TraesCS7B01G454300 chr2B 92.191 461 34 2 184 643 763334029 763333570 0.000000e+00 651
28 TraesCS7B01G454300 chr6A 91.684 469 37 2 178 645 588045766 588046233 0.000000e+00 649
29 TraesCS7B01G454300 chr3B 94.558 294 16 0 3102 3395 284636949 284637242 4.210000e-124 455
30 TraesCS7B01G454300 chr3B 94.422 251 14 0 2851 3101 284636647 284636897 1.560000e-103 387
31 TraesCS7B01G454300 chr3B 97.175 177 5 0 3398 3574 284637279 284637455 2.090000e-77 300


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G454300 chr7B 715080741 715084314 3573 True 6601.000000 6601 100.000000 1 3574 1 chr7B.!!$R2 3573
1 TraesCS7B01G454300 chr7B 715152809 715156390 3581 True 6325.000000 6325 98.577000 1 3574 1 chr7B.!!$R4 3573
2 TraesCS7B01G454300 chr7B 715120128 715123710 3582 True 6303.000000 6303 98.465000 1 3574 1 chr7B.!!$R3 3573
3 TraesCS7B01G454300 chr7B 714898465 714902014 3549 True 5934.000000 5934 96.765000 2 3574 1 chr7B.!!$R1 3572
4 TraesCS7B01G454300 chr7B 715320709 715322453 1744 True 1938.000000 1938 86.901000 812 2575 1 chr7B.!!$R5 1763
5 TraesCS7B01G454300 chr7B 714945713 714950696 4983 True 1720.333333 3040 94.694333 1 3574 3 chr7B.!!$R7 3573
6 TraesCS7B01G454300 chr7B 714843832 714845000 1168 True 571.666667 905 93.138333 2348 3574 3 chr7B.!!$R6 1226
7 TraesCS7B01G454300 chr4A 700428049 700430978 2929 True 1206.333333 3302 96.350667 1 2850 3 chr4A.!!$R1 2849
8 TraesCS7B01G454300 chr7D 619581941 619583749 1808 False 2012.000000 2012 87.039000 769 2572 1 chr7D.!!$F1 1803
9 TraesCS7B01G454300 chr7D 620583009 620584806 1797 False 1925.000000 1925 86.272000 769 2572 1 chr7D.!!$F2 1803
10 TraesCS7B01G454300 chr7D 619358752 619359590 838 True 624.500000 667 92.343000 730 1541 2 chr7D.!!$R3 811
11 TraesCS7B01G454300 chr7D 495333218 495333978 760 True 550.000000 819 94.440000 2850 3574 2 chr7D.!!$R2 724
12 TraesCS7B01G454300 chr7A 713833345 713835170 1825 False 2001.000000 2001 86.818000 769 2572 1 chr7A.!!$F1 1803
13 TraesCS7B01G454300 chrUn 93248559 93249919 1360 True 1535.000000 1535 87.303000 734 2096 1 chrUn.!!$R1 1362
14 TraesCS7B01G454300 chr3B 284636647 284637455 808 False 380.666667 455 95.385000 2851 3574 3 chr3B.!!$F1 723

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
929 1986 1.539869 CGATCCCATCCCCATCCCT 60.540 63.158 0.0 0.0 0.0 4.20 F
1131 2231 3.853330 CGTGCCGCCATGTCTTCG 61.853 66.667 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 4836 0.317479 CCGGTCTCAAAGTCGGAGTT 59.683 55.0 0.0 0.0 44.69 3.01 R
2638 5673 2.028020 ACAGCCTTCTTCCTAAACTCGG 60.028 50.0 0.0 0.0 0.00 4.63 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
571 1149 7.433131 CACGTTGTAAGTTAGTTGAAGAGTACA 59.567 37.037 0.00 0.00 0.00 2.90
585 1163 9.477484 GTTGAAGAGTACAGATCTCAAAGTAAA 57.523 33.333 0.00 0.00 34.73 2.01
600 1178 2.621070 AGTAAAGCTGGAGGGTTGAGA 58.379 47.619 0.00 0.00 35.65 3.27
775 1826 1.557651 GTCAACGAGATTAGGTCGGC 58.442 55.000 0.00 0.00 41.88 5.54
846 1903 8.771766 GGTAAGAAGTTTGAATCGAAGTTAACT 58.228 33.333 1.12 1.12 0.00 2.24
929 1986 1.539869 CGATCCCATCCCCATCCCT 60.540 63.158 0.00 0.00 0.00 4.20
1131 2231 3.853330 CGTGCCGCCATGTCTTCG 61.853 66.667 0.00 0.00 0.00 3.79
1820 4836 1.655484 CGGCAATGACTACATGAGCA 58.345 50.000 0.00 0.00 38.91 4.26
2468 5503 1.153353 GCGAAAATCCCGACAAGACA 58.847 50.000 0.00 0.00 0.00 3.41
2620 5655 4.630894 TGGCGCAATATCTTTTAGGTTG 57.369 40.909 10.83 0.00 0.00 3.77
2638 5673 9.569122 TTTAGGTTGGCTGTTATAAATAGGATC 57.431 33.333 0.00 0.00 0.00 3.36
2748 5783 7.115236 GGTTAAACATGAACGGGTGTTAATTTC 59.885 37.037 0.00 0.00 38.78 2.17
2842 5884 7.148641 CGTGATAACTCTAATCAGTAGGCATT 58.851 38.462 0.00 0.00 34.12 3.56
2931 5988 0.264657 AGAAAAAGGTGGGGTTGCCT 59.735 50.000 0.00 0.00 36.51 4.75
2994 6051 1.876156 GTCTCAACCTGGAAGTTGCTG 59.124 52.381 0.00 0.00 45.47 4.41
3338 6457 5.477984 ACTGCATTGATCCACTGTAATGTTT 59.522 36.000 0.00 0.00 34.04 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
542 1120 7.222224 ACTCTTCAACTAACTTACAACGTGAAG 59.778 37.037 0.00 0.0 0.00 3.02
571 1149 4.080638 CCCTCCAGCTTTACTTTGAGATCT 60.081 45.833 0.00 0.0 29.66 2.75
585 1163 3.454082 CTCTTATTCTCAACCCTCCAGCT 59.546 47.826 0.00 0.0 0.00 4.24
600 1178 5.216622 TCAGGCTACATGGTACCTCTTATT 58.783 41.667 14.36 0.0 0.00 1.40
775 1826 1.712081 CGCTGGAGCATGTCTTTCG 59.288 57.895 0.00 0.0 42.21 3.46
846 1903 2.176889 GTACCTTAGTGTCCTGCTCCA 58.823 52.381 0.00 0.0 0.00 3.86
929 1986 2.443449 TGATGGAGAGGGAGGGAGATA 58.557 52.381 0.00 0.0 0.00 1.98
1820 4836 0.317479 CCGGTCTCAAAGTCGGAGTT 59.683 55.000 0.00 0.0 44.69 3.01
2468 5503 2.567615 GTGTGTCTGGTCCCAGTAGAAT 59.432 50.000 12.88 0.0 43.96 2.40
2620 5655 6.038997 ACTCGGATCCTATTTATAACAGCC 57.961 41.667 10.75 0.0 0.00 4.85
2638 5673 2.028020 ACAGCCTTCTTCCTAAACTCGG 60.028 50.000 0.00 0.0 0.00 4.63
2723 5758 7.149096 CGAAATTAACACCCGTTCATGTTTAAC 60.149 37.037 0.00 0.0 39.67 2.01
2748 5783 8.617290 ACTAACAGGGGATAAAATAATAAGCG 57.383 34.615 0.00 0.0 0.00 4.68
2842 5884 4.005650 CGCGTACCCCTCTAGTCATATAA 58.994 47.826 0.00 0.0 0.00 0.98
2931 5988 4.078537 TCGAAAAATCCTGAAATGAGGCA 58.921 39.130 0.00 0.0 32.51 4.75
2994 6051 6.088616 GTGCAAATTCAGCAACTCTTGAATAC 59.911 38.462 7.06 0.0 44.64 1.89
3338 6457 8.286800 CCTGAAATTGTTGTTCGTGAGTAAATA 58.713 33.333 0.00 0.0 0.00 1.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.